Why are objects rotation rotated a little bit when they are set to 0?
All terms of the orientation matrix are expressed in float values (floating point numbers). These numbers have a specific precision. This means when you calculate with them you get very small, but existing deviations from the "ideal" number. 

This is especially noticeable around zero. Therefore you might print something like -0.0. This seams illogical but it means you have a number that is smaller than the precision of the formatter.

Unfortunately you did not include any further details such as what term you are reading and what the value is or what your code is. 

My own investigation shows me:

&lt;Matrix 3x3 ( 1.0000, 0.0000, 0.0000)
            ( 0.0000, 1.0000, 0.0000)
            (-0.0000, 0.0000, 1.0000)&gt;


The [2][0] value is indeed -0, but it has no further consequences. You will not notice that in your scene.